According to evolutionists, they are our closest cousins on their imaginary tree of life. While it is true that humans and chimpanzees share a lot of DNA, this is to be expected, as they use the same genetic code.
Even with separate creations by God, as long as he is using a single genetic code, there will be genetic similarities among different kinds. One of the big misconceptions that is claimed as evidence for common descent is the presupposition that an independent origin, even a divine one, would result in totally different genetic languages. However, this is not necessarily true, particularly if you are designing organisms that can eat the same foods. It turns out, however, that comparisons of the human and chimpanzee Y chromosomes reveal significant differences that tend to contradict the idea of a common ancestor.
General comparison of human and chimp DNA.
A superficial comparison between human and chimpanzee DNA shows some similarities and differences. Evolutionists frequently claim that human and chimpanzee DNA are 98.8% similar. However, two critical factors were missing in the original claim. The first is that this figure originates from a study that excluded 25% of the human genome and 18% of the chimpanzee genome because they could not be aligned. Now, when counting only substitutions, where one nucleotide replaces another, they found approximately 98.8% of their DNA. However, when considering insertions and deletions, the shared DNA drops to about 96%. When the parts that cannot be aligned are considered, the similarity immediately drops to at best 87%. But it gets even worse: more recent research puts this number at about 85% similarity.
Initial comparison of the human and chimp Y Chromosome.
An initial surface-level comparison of the human and chimpanzee Y chromosomes reveals a significant difference between them. The most obvious difference is that the chimpanzee Y chromosome is significantly shorter than that of humans, gorillas, and orangutans. While this is a superficial initial comparison, it is significant.
You have to remember that chimpanzees are supposed to be our closest evolutionary cousins. The fact that there is such a significant difference, even at a superficial level, challenges this claim. Furthermore, as we dive deeper into this question, the evidence is going to present an even bigger challenge to this claim of humans and chimpanzees being related.
Comparison of chimpanzee and human Y chromosomes
A recent study comparing the human and chimpanzee Y chromosomes produced results that were surprising but are fully expected from a creationist perspective. The first thing to note from this study is that only 14% to 27% of chimp Y chromosome sequences align with the human Y chromosome, indicating substantial differences. In other words, the closest they could be based on this simple fact is 86% similar, which is a very large starting point for two species that are supposed to be closely related.
The Y chromosome is the one chromosome passed down exclusively from father to son. This is also one of the reasons why it is a very good check for lineage: unlike the other chromosomes, it does not undergo recombination. This means that other than mutations, the Y chromosome is passed down from father to son completely intact.
Gene Comparison of the chimpanzee and human Y Chromosomes.
The problem gets even worse when you do a comparison of the chimpanzee and human Y Chromosomes By comparing genes. This is because the Human Y chromosome has more than twice as many genes as that of a chimpanzee. This is a very significant difference that goes against the idea of common descent, but it's fully expected from a creationist perspective.
When you look at the X degenerate genes, humans have 16, while chimpanzees only have 12. This is a difference of four genes, resulting in a similarity of just 75%. While this is a significant difference that goes against common descent, it gets even worse when we look at other types of genes in the two Y chromosomes.
When you look at the Ampliconic genes, humans have 60, while chimpanzees only have 25, for a difference of 35 genes. Humans pick up an additional two genes when we look at X-Transposed genes. In total, humans have 78, while chimpanzees only have 37, resulting in a difference of 41 genes. This results in a similarity of only 47% in terms of genes and 67% in terms of gene families. These are really significant differences.
Analysis of the Comparison of the Chimpanzee and Human Y Chromosomes.
This comparison of the Human and chimpanzee Y chromosomes is extremely significant. Not only is the chimpanzee's Y chromosome significantly shorter than its human counterpart, but only about 14% of the human why chromosome can be aligned with the chimpanzee’s. Furthermore, chimpanzee Y chromosomes have fewer than half the genes of the human Y chromosomes. This is a huge difference.
The differences between the human and chimpanzee Y chromosomes are so significant that they argue against common ancestry. The problem is that evolutionists see any similarity as evidence in favor of common descent because they assume a separate origin would be random. They even make this assumption when discussing ideas such as an intelligent designer.
Conclusion
The ultimate question is, does this evidence falsify the idea of universal common descent? Well, the answer is no, but not for the right reasons. The simple fact of the matter is that universal common descent is an absolute necessity from the perspective of absolute atheistic naturalism. Consequently, there is no evidence whatsoever that will be allowed to falsify this perspective on biological history. Such evidence would either simply be ignored or an untestable just-so story would be invented to explain it away. The simple fact of the matter is that, regardless of the evidence, universal common descent will never be allowed to be falsified; therefore, this is why chromosome evidence does not and cannot falsify universal common descent. However. It is a strong argument against it.
----------------------------------
References
Initial sequence of the chimpanzee genome and comparison with the human genome
https://www.nature.com/articles/nature04072
Fact Check: New “Complete” Chimp Genome Shows 14.9 Percent Difference from Human Genome
Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content
